ReviewJournal of applied genetics2016
Review of alignment and SNP calling algorithms for next-generation sequencing data.
Review in Journal of applied genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- A Boruta-SMOTE Integrated Approach for Rapid Donkey Breed Classification Using SNP Data: Addressing High-Dimensionality and Small Sample Challenges.Biochemical genetics · 2026Article
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- Genomic evidence of sex chromosome aneuploidy and infection-associated genotypes in the tsetse fly Glossina fuscipes, the major vector of African trypanosomiasis in Uganda.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2023Article
- Identification of QTL under Brassinosteroid-Combined Cold Treatment at Seedling Stage in Rice Using Genotyping-by-Sequencing (GBS).Plants (Basel, Switzerland) · 2022Article
- High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing.Plant methods · 2022Article
- Quantitative Trait Loci Mapping Analysis for Cold Tolerance Under Cold Stress and Brassinosteroid-Combined Cold Treatment at Germination and Bud Burst Stages in Rice.Frontiers in plant science · 2022Article
- Comparison of sequencing data processing pipelines and application to underrepresented African human populations.BMC bioinformatics · 2021Article
- SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants.Microbiology spectrum · 2021Article
- Simulation of African and non-African low and high coverage whole genome sequence data to assess variant calling approaches.Briefings in bioinformatics · 2021Article
- Review
- Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era.Methods in molecular biology (Clifton, N.J.) · 2021Review
- High-Throughput Genotyping Technologies in Plant Taxonomy.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.GigaScience · 2020Article
- Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies).Genome biology and evolution · 2020Article
- Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance.Frontiers in genetics · 2020Review
- Population Genomics of Fungal Plant Pathogens and the Analyses of Rapidly Evolving Genome Compartments.Methods in molecular biology (Clifton, N.J.) · 2020Article
- PVCTools: parallel variation calling tools.Heliyon · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Application of the massive parallel sequencing technology has become one of the most important issues in life sciences. Therefore, it was crucial to develop bioinformatics tools for next-generation sequencing (NGS) data processing. Currently, two of the most significant tasks include alignment to a reference genome and detection of single nucleotide polymorphisms (SNPs). In many types of genomic analyses, great numbers of reads need to be mapped to the reference genome; therefore, selection of the aligner is an essential step in NGS pipelines. Two main algorithms-suffix tries and hash tables-have been introduced for this purpose. Suffix array-based aligners are memory-efficient and work faster than hash-based aligners, but they are less accurate. In contrast, hash table algorithms tend to be slower, but more sensitive. SNP and genotype callers may also be divided into two main different approaches: heuristic and probabilistic methods. A variety of software has been subsequently developed over the past several years. In this paper, we briefly review the current development of NGS data processing algorithms and present the available software.
Indexed as
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.